Michael Bede Cranston, 59, is charged with two Commonwealth offences of using information obtained in his capacity as a public official and exercising influence in his capacity as a public official.

The 35-year veteran of the ATO, who was considered to have an "illustrious" career until he was charged on May 17, has been suspended while the criminal matter is afoot.

He has since chosen to resign, effective from Tuesday.

Police allege he tried to access restricted ATO information on behalf of his son, Adam Cranston, who was allegedly running the fraudulent scheme.

Two ATO assistant commissioners, Tony Poulakis and Scott Burrows, who were allegedly directed by Mr Cranston to look up information, have also been stood down.

Police don't believe Mr Cranston had any knowledge of the tax fraud syndicate his children were allegedly involved in but he allegedly attempted to access information on garnishee orders on various companies and on an ATO audit on the payroll business at the centre of the scheme.

In an intercepted phone call in late January, Adam Cranston told tax lawyer and alleged syndicate member Dev Menon that he was getting his father to "look into" garnishee orders served on some of their companies

"He is looking into it but considering he doesn't know about it, it can't be like the biggest thing since Ben Hur," Adam Cranston allegedly told Mr Menon.

Adam and Lauren Cranston are among nine people charged with running the alleged tax fraud scheme that skimmed $130 million through a web of payroll administration companies.

On Tuesday, Michael and Lauren Cranston appeared in the Downing Centre Local Court for the first mention of their criminal charges.

Prosecutor David Moorhouse said the brief of evidence would be served on their lawyers by August 8 and the matter would return to court on August 29.

They were both excused from appearing next time if legally represented, with the court hearing that Lauren Cranston, 24, is due to give birth at the end of July.

She had a separate hearing in the NSW Supreme Court on Tuesday as part of a proceeds of crime case launched by the Australian Federal Police.

Ms Cranston will undergo a compulsory examination of her financial situation in the Administrative Appeals Tribunal later on Tuesday.

After initially flagging that she would challenge the examination, her lawyer said that she was "prepared to give [it] a go".

The AFP is attempting to claw back money from 68 individuals and companies connected to the investigation. Michael Cranston will undergo a compulsory examination later this month.

Following the arrests in May, ATO acting commissioner Andrew Mills said Mr Cranston was one of the organisation's "long-serving senior officers" who had "quite an illustrious [career] up until this point".

He said he was confident the Tax Office's systems had not been compromised nor breached and the accused employees were not able to obtain any information.

On Tuesday, an ATO spokeswoman said: "We can confirm Michael Cranston has chosen to resign his Deputy Commissioner role at the ATO effective 13 June 2017."

Police allege the syndicate spent much of the money on luxury goods. Among the items seized under proceeds of crime were 25 motor vehicles, including luxury cars and racing cars, 12 motorbikes, 18 residential properties, two aircraft, $1 million from a safe deposit box, firearms, jewellery, bottles of Grange wine and artworks.

with Michaela Whitbourn